Should I upload my assemblies to NCBI Genbank, Genome or WGS?
I have complete (every structure in 1 contig) and fragmented (every structure in multiple contigs) assemblies of bacteria that are part of 1 Bioproject/study.
But I am not sure if I should upload these assemblies to NCBI genbank, Genome or WGS batch.
Or should I upload all complete assemblies to Genbank and the fragmented ones to WGS?
Or is there not really a difference between the three types of submission?
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If you are certain of the quality of the assembly (where you have a single contig) then you can upload them doing Prokaryotic annotation pipeline submitting through Genome submissions portal. Fragmented ones are probably more appropriate for WGS. Email NCBI/ENA help desk and ask.